It was honorable. He was originally processed for a general, but it was upgraded to honorable.
Ref: http://www.washingtontimes.com/news/2013/sep/17/honorable-discharge-navy-yard-shooter-who-had-patt/
also: http://www.military.com/daily-news/2013/09/17/navy-yard-gunman-had-honorable-discharge.html